Chapter 15 Chapter 15 EnzymesEnzymes

EnzymesEnzymesRibbon diagram of cytochrome c oxidase, the enzyme that directly uses oxygen during respiration.

Enzyme CatalysisEnzyme CatalysisEnzymeEnzyme:: A biological catalyst.• With the exception of some RNAs that catalyze their

own self-cleavage, all enzymes are proteins.

• Enzymes can increase the rate of a reaction by a factor of 109 to 1020 over an uncatalyzed reaction.

• Some catalyze the reaction of only one compound.

• Others are stereoselective; for example, enzymes that catalyze the reactions of only L-amino acids.

• Others catalyze reactions of specific types of compounds or bonds; for example, trypsin catalyzes hydrolysis of peptide bonds formed by the carboxyl groups of Lys and Arg.

Enzyme CatalysisEnzyme CatalysisFigure 15.1 Trypsin catalyzes the hydrolysis of peptide bonds formed by the carboxyl group of lysine and arginine.

Classification of EnzymesClassification of EnzymesEnzymes are commonly named after the reaction or reactions they catalyze.• Example: lactate dehydrogenase, acid

phosphatase.

Enzymes are classified into six major groups according to the type of reaction catalyzed:• Oxidoreductases:Oxidoreductases: Oxidation-reduction

reactions.• Transferases:Transferases: Group transfer reactions.• Hydrolases:Hydrolases: Hydrolysis reactions.• LyasesLyases:: Addition of two groups to a double

bond, or removal of two groups to create a double bond.

• Isomerases:Isomerases: Isomerization reactions.• Ligases:Ligases: The joining to two molecules.

Classification of EnzymesClassification of Enzymes1. Oxidoreductase:

2. Transferase:

Classification of EnzymesClassification of Enzymes

3. Hydrolase:

4. Lyase:

Classification of EnzymesClassification of Enzymes5. Isomerase:

6. Ligase:

Enzyme TerminologyEnzyme TerminologyApoenzyme:Apoenzyme: The protein part of an enzyme.

Cofactor:Cofactor: A nonprotein portion of an enzyme that is necessary for catalytic function; examples are metallic ions such as Zn2+ and Mg2+.

Coenzyme:Coenzyme: A nonprotein organic molecule, frequently a B vitamin, that acts as a cofactor.

Substrate:Substrate: The compound or compounds whose reaction an enzyme catalyzes.

Active site:Active site: The specific portion of the enzyme to which a substrate binds during reaction.

Schematic of an Active Schematic of an Active SiteSite

Figure 15.2 Schematic diagram of the active site of an enzyme and the participating components.

Terms in Enzyme Terms in Enzyme ChemistryChemistryActivation:Activation: Any process that initiates or increases the

activity of an enzyme.

Inhibition:Inhibition: Any process that makes an active enzyme less active or inactive.

Competitive inhibitor:Competitive inhibitor: A substance that binds to the active site of an enzyme thereby preventing binding of substrate.

Noncompetitive inhibitor:Noncompetitive inhibitor: Any substance that binds to a portion of the enzyme other than the active site and thereby inhibits the activity of the enzyme.

Enzyme ActivityEnzyme ActivityEnzyme activity:Enzyme activity: A measure of how much a reaction rate is increased.

We examine how the rate of an enzyme-catalyzed reaction is affected by:• Enzyme concentration.• Substrate concentration. • Temperature.• pH.

Enzyme ActivityEnzyme Activity

Figure 15.3 The effect of enzyme concentration on the rate of an enzyme-catalyzed reaction. Substrate concentration, temperature, and pH are constant.

Enzyme ActivityEnzyme ActivityFigure 15.4 The effect of substrate concentration on the rate of an enzyme-catalyzed reaction. Enzyme concentration, temperature, and pH are constant.

Enzyme ActivityEnzyme ActivityFigure 15.5 The effect of temperature on the rate of an enzyme-catalyzed reaction. Substrate and enzyme concentrations and pH are constant.

Enzyme ActivityEnzyme ActivityFigure 15.6 The effect of pH on the rate of an enzyme-catalyzed reaction. Substrate and enzyme concentrations and temperature are constant.

Mechanism of ActionMechanism of Action

Figure 15.7 Lock-and-key model of enzyme mechanism.

• The enzyme is a rigid three-dimensional body.• The enzyme surface contains the active site.

Mechanism of ActionMechanism of ActionFigure 15.8 The Induced-fit model of an enzyme

mechanism.• The active site becomes modified to accommodate

the substrate.

Mechanism of ActionMechanism of ActionFigure 23.9 The mechanism of competitive inhibition.

When a competitive inhibitor enters the active site, the substrate cannot enter.

Mechanism of ActionMechanism of ActionFigure 15.10 Mechanism of noncompetitive inhibition. The inhibitor binds itself to a site other than the active site (allosterism), thereby changing the conformation of the active site. The substrate still binds but there is no catalysis.

Mechanism of ActionMechanism of Action

Figure 15.11 Enzyme kinetics in the presence and the absence of inhibitors.

Mechanism of ActionMechanism of Action• Both the lock-and-key model and the induced-fit

model emphasize the shape of the active site.• However, the chemistry of the active site is the most

important.• Just five amino acids participate in the active site in

more than 65% of the enzymes studied to date.• These five are His > Cys > Asp > Arg > Glu.• Four of these amino acids have either acidic or basic

side chains; the fifth has a sulfhydryl group (-SH).

Catalytic PowerCatalytic Power• Figure 15.12 Enzymes provide an alternative pathway for

reaction. (a) The activation energy profile for a typical reaction. (b) A comparison of the activation energy profiles for a catalyzed and uncatalyzed reactions.

Enzyme RegulationEnzyme RegulationFeedback control:Feedback control: An enzyme-regulation process where the product of a series of enzyme-catalyzed reactions inhibits an earlier reaction in the sequence.

• The inhibition may be competitive or noncompetitive.

Enzyme RegulationEnzyme Regulation• Proenzyme (zymogen):Proenzyme (zymogen): An inactive form of an enzyme

that must have part of its polypeptide chain hydrolyzed and removed before it becomes active.• An example is trypsin, a digestive enzyme.• It is synthesized and stored as trypsinogen, which has

no enzyme activity.• It becomes active only after a six-amino acid fragment

is hydrolyzed and removed from the N-terminal end of its chain.

• Removal of this small fragment changes not only the primary structure but also the tertiary structure, allowing the molecule to achieve its active form.

Enzyme RegulationEnzyme RegulationAllosterism:Allosterism: Enzyme regulation based on an event occurring at a place other than the active site but that creates a change in the active site.• An enzyme regulated by this mechanism is

called an allosteric enzymeallosteric enzyme.• Allosteric enzymes often have multiple

polypeptide chains.• Negative modulation:Negative modulation: Inhibition of an

allosteric enzyme.• Positive modulation:Positive modulation: Stimulation of an

allosteric enzyme. • Regulator:Regulator: A substance that binds to an

allosteric enzyme.

Enzyme RegulationEnzyme Regulation• Figure 15.14 The

allosteric effect. Binding of the regulator to a site other than the active site changes the shape of the active site.

Enzyme RegulationEnzyme Regulation

Figure 15.15 Effects of binding activators and inhibitors to allosteric enzymes. The enzyme has an equilibrium between the T form and the R form.

Enzyme RegulationEnzyme RegulationProtein modification:Protein modification: The process of affecting enzyme activity by covalently modifying it.• The best known examples of protein modification

involve phosphorylation/dephosphorylation.• Example: Pyruvate kinase (PK) is the active form of

the enzyme; it is inactivated by phosphorylation to pyruvate kinase phosphate (PKP).

Enzyme RegulationEnzyme RegulationIsoenzyme (Isozymes):Isoenzyme (Isozymes): An enzyme that occurs in multiple forms; each catalyzes the same reaction.• Example: lactate dehydrogenase (LDH) catalyzes

the oxidation of lactate to pyruvate.• The enzyme is a tetramer of H and M chains.

• H4 is present predominately in heart muscle.

• M4 is present predominantly in the liver and in skeletal muscle.

• H3M, H2M2, and HM3 also exist.

• H4 is allosterically inhibited by high levels of pyruvate while M4 is not.

• H4 in serum correlates with the severity of heart attack.

Enzyme RegulationEnzyme RegulationFigure 15.16 The isozymes of lactate dehydrogenase (LDH). The electrophoresis gel depicts the relative isozyme types found in different tissues.

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Enzymes Used in MedicineEnzymes Used in Medicine

Insert Table 23.2, page 648

Table 15.2 – Enzyme Assays useful in Medical Diagnosis

Transition-State AnalogsTransition-State Analogs• Transition state analogTransition state analog: A molecule whose shape

mimics the transition state of a substrate.• Abzyme:Abzyme: An antibody that has catalytic activity because

it was created using a transition state analog as an immunogen. (a) The molecule below is a transition analog for the reaction of an amino acid with pyridoxal-5’-phosphate.

Transition-State AnalogsTransition-State Analogs

The abzyme is then used as a catalyst

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Catalytic Antibodies Against Catalytic Antibodies Against CocaineCocaine

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Catalytic Antibodies Against Cocaine